Incorporated Bowo's suggestions.

README.md

-# Project skeleton
-A skeleton Git repository for analysis projects.
+# Cookiecutter for data analysis projects
+Set up a SASC data analysis project.
 
-# Preparations
+## Preparations
 Install dependencies.
 
+    apt-get install git-annex
+
     pip install -r https://git.lumc.nl/sasc/cookiecutter-data-analysis/raw/master/requirements.txt
 
 Configure Cookiecutter by editing `.cookiecutterrc` in your home directory.
@@ -11,9 +13,9 @@ Configure Cookiecutter by editing `.cookiecutterrc` in your home directory.
 ```yml
 ---
 default_context:
-  full_name: Your Name
-  email: UserName@lumc.nl
-cookiecutters_dir: /path/to/cookiecutters/
+  full_name: John Doe
+  email: J.Doe@lumc.nl
+cookiecutters_dir: /tmp
 ```
 
 Configure Python GitLab by editing `.python-gitlab.cfg` in your home directory.
@@ -27,43 +29,10 @@ Configure Python GitLab by editing `.python-gitlab.cfg` in your home directory.
     url = https://git.lumc.nl
     private_token = your_token_here
 
-# Starting a project
-To start a new analysis project based on this skeleton, use the following
-command.
-
-    cookiecutter https://git.lumc.nl/sasc/cookiecutter-data-analysis.git
-
-## Working together on the same clone
-If you need to work with other people on the same repository clone on the Shark cluster, you can use the following command to give group access:
-
-    find -type d -exec chmod 775 {} \;
-    find -type f -exec chmod 664 {} \;
-
-## Cloning to a portable disk (NTFS)
-Presuming your disk is attached to your own computer and the repository is on
-the Shark cluster, you can use the following commands.
-
-    git clone ssh://shark/path/to/project/my-project
-    cd my-project
-
-For some reason `annex-ignore` is set to `true`, we need to set it to `false`.
+The `private_token` is the only variable you need to set. You can find your
+private token [here](https://git.lumc.nl/profile/account).
 
-    git config remote.origin.annex-ignore false
+## Starting a project
+To start a new data analysis project, use the following command:
 
-Set the repository to *direct mode* to prevent making symlinks, otherwise it
-will be very difficult for windows users to access the files.
-
-    git annex direct
-
-SSH caching seems to be broken on NTFS.
-
-    git config annex.ssh-options "-S /tmp/ssh_mux_%h_%p_%r"
-
-Or alternatively, disable SSH caching all together (slow when working with a
-large number of files).
-
-    git config annex.sshcaching false
-
-Get the content.
-
-    git annex get .
+    cookiecutter https://git.lumc.nl/sasc/cookiecutter-data-analysis.git

cookiecutter.json

@@ -2,11 +2,12 @@
     "full_name": "Jeroen F.J. Laros",
     "email": "J.F.J.Laros@lumc.nl",
     "client_full_name": "John Doe",
-    "client_email": "J.Doe@lumc.nl",
+    "client_email": "{{ cookiecutter.client_full_name.split()[0][0] + '.' + ''.join(cookiecutter.client_full_name.split()[1:]) }}@lumc.nl",
+    "client_username": "{{ cookiecutter.client_email.split('@')[0]|lower }}",
     "sequencing_centre": "LGTC",
     "sequencing_platform": "Illumina HiSeq 2500",
-    "molecular_type": "RNA",
     "experiment_type": "RNASeq",
-    "project_name": "jdoe-rnaseq",
-    "namespace": "sasc"
+    "project_number": 1,
+    "project_name": "project-{{ cookiecutter.project_number }}-{{ cookiecutter.experiment_type|lower }}-{{ cookiecutter.client_username.replace('.', '') }}",
+    "gitlab_repo_namespace": "sasc"
 }

hooks/post_gen_project.sh

@@ -4,7 +4,7 @@ get_value() {
   grep "$1: " | cut -f 2 -d ' '
 }
 
-namespace={{ cookiecutter.namespace }}
+namespace={{ cookiecutter.gitlab_repo_namespace }}
 namespace_id=$(gitlab group search --query $namespace | get_value id)
 namespace_opt=""
 if [ $namespace_id ]; then
@@ -16,7 +16,23 @@ fi
 git init
 git add .
 git commit -m "Initial commit."
-gitlab project create --name {{ cookiecutter.project_name }} $namespace_opt
+project_id=$(
+  gitlab project create \
+    --name {{ cookiecutter.project_name }} $namespace_opt | get_value id)
 git remote add origin \
   git@git.lumc.nl:$namespace/{{ cookiecutter.project_name }}.git
 git push --set-upstream origin master
+
+client_id=$(
+  gitlab user search --query {{ cookiecutter.client_username }} | get_value id)
+if [ $client_id ]; then
+  gitlab project-member create \
+    --project-id $project_id --user-id $client_id --access-level 30
+else
+  cat << EOF
+
+Could not add client to the project.
+
+    https://git.lumc.nl/$namespace/{{ cookiecutter.project_name }}.git
+EOF
+fi

requirements.txt

-cookiecutter
-python-gitlab
+cookiecutter==1.4.0
+python-gitlab==0.14

{{ cookiecutter.project_name }}/README.md

 # General information
 {{ cookiecutter.experiment_type }} data analysis for {{ cookiecutter.client_full_name }}.
 
+See the [ticket](https://humgenprojects.lumc.nl/trac/sasc/ticket/{{ cookiecutter.project_number }}) for the original request.
+
+Project started on: {% now 'local', '%a %b %d, %Y' %}.  
+Project finished on: 
+
 ## Contact information
 Owner: {{ cookiecutter.client_full_name }} <{{ cookiecutter.client_email }}>  
 Project leader: {{ cookiecutter.full_name }} <{{ cookiecutter.email }}>  

{{ cookiecutter.project_name }}/data/README.md

@@ -5,7 +5,6 @@ sequencing centre). Also see *Notes* below.
 ## Details
 Sequencing centre: {{ cookiecutter.sequencing_centre }}  
 Platform: {{ cookiecutter.sequencing_platform }}  
-Molecular type: {{ cookiecutter.molecular_type }}  
 Experiment type:  {{ cookiecutter.experiment_type }}  
 Owner: {{ cookiecutter.client_full_name }} <{{ cookiecutter.client_email }}>  
 Data gathered by: {{ cookiecutter.full_name }} <{{ cookiecutter.email }}>  
@@ -26,3 +25,38 @@ now do `git commit` as normal.
 
 For more information, please see the
 [Git-annex walkthrough](http://git-annex.branchable.com/walkthrough/).
+
+### Working together on the same clone
+If you need to work with other people on the same repository clone on the Shark cluster, you can use the following command to give group access:
+
+    find -type d -exec chmod 775 {} \;
+    find -type f -exec chmod 664 {} \;
+
+### Cloning to a portable disk (NTFS)
+Presuming your disk is attached to your own computer and the repository is on
+the Shark cluster, you can use the following commands.
+
+    git clone ssh://shark/exports/{{ cookiecutter.gitlab_repo_namespace }}/{{ cookiecutter.project_name }}
+    cd my-project
+
+For some reason `annex-ignore` is set to `true`, we need to set it to `false`.
+
+    git config remote.origin.annex-ignore false
+
+Set the repository to *direct mode* to prevent making symlinks, otherwise it
+will be very difficult for windows users to access the files.
+
+    git annex direct
+
+SSH caching seems to be broken on NTFS.
+
+    git config annex.ssh-options "-S /tmp/ssh_mux_%h_%p_%r"
+
+Or alternatively, disable SSH caching all together (slow when working with a
+large number of files).
+
+    git config annex.sshcaching false
+
+Get the content.
+
+    git annex get .